Anathema
by dripping-glass
Summary: Upon reopening the file for Project Shadow, a new team of scientists decides to pick up where the experiments on the ARK left off. Shadow's back in the hell he thought he'd never have to experience again, and the scientists use Shadow's power to throw everyone into a world of fear, power, and of course, chaos. Soon, the entire world turns against those it once idolized. /Sonadow
1. Intro

_-The only thing necessary for the triumph of evil is for good men to do nothing.-_

* * *

Edmund Burke


	2. Uniforms

Sonic POV_

Waking up before Shadow is always weird, but usually welcome. I don't feel like leaving the warmth of the bed and the blankets tangled all around me, but working here at the Mobian Protection Agency, sacrifices must be made. ...even if that means getting out of bed before 2 pm every day. I open my eyes. Sunlight is flooding the room, as the sun always rises on this side of the agency building. Judging from the pink and sunburn-tinted sky, it's still pretty early.

I sit up and see Shadow on the opposite side of the bed, turned away from me. His breathing is so slow, sometimes I wonder if he's dead. I think if I should bother him or not, and of course I decide that I should. I reach over and touch his shoulder lightly, and I receive no response. My hand moves slowly down his shoulder, disappears under the single blanket he has over him, and travels beyond his elbow, down to his wrist, and stops on his left Inhibitor ring.

"Mmh," he growls absently, lazily pulling his arm away from me. He turns slightly more, and pulls his fist up against his stomach in an attempt to ward me off. I smile at him and I get up to shower. I have to help Tails in the infirmary today.

* * *

"Do you realize how close they were to fully utilizing his full potential?" a middle-aged man with light brown hair asks, keeping his voice low. It was a little pointless though, considering these men were alone.

"Of course I do! I've read the documents. Do you realize how illegal it would be to resurrect this whole thing? Our licenses could be revoked!" the other says to his older colleague. Both of them work for GUN, and for several weeks, Professor Seller has been going on and on about this old file. Everyone has heard of it, but so few people have looked into it as deeply as Seller.

"Ah, that," the first one waves his hand dismissively. He points directly at the file with black ink across the front. It has thirteen letters across the front, followed by a messy signature reading 'Professor Gerald Robotnik'. "Professor Black, I assure you... I am absolutely positive the recognition and achievements we could attain will be exponentially more valuable than our licenses. You know as well as I do, GUN never wanted this project shut down."

The younger scientist sighs deeply, feeling uneasy about the intensity this man has. All of this is such sensitive territory. Discussing it so openly is like walking on thin, fragile glass. He couldn't honestly say he wasn't intrigued by the idea of picking up the experiments, though, and Seller was using this appeal to persuade Black into agreeing to reopen the file.

"We know where he is. We know exactly where to conduct everything! The only thing holding up this operation is your lack of nerve. What scientist isn't willing to try controversial things?" Seller asks. "All I need is your affirmation, and our teams will combine. We'll all swear to confidentiality and we'll have surplus intelligence. What could go wrong?"

Black shakes his head, unfortunately lured by the suggestion."He could be stronger now. He remembers what happened. What makes you think he'd be so willing to cooperate?"

"How do you think they made him cooperate before?" Sellers asks, shoulders high in a shrug. "The scientists up there, they made drugs specifically for his system just to manipulate him! We have it already. My team has been working on it. So far, the tests we've done have all worked just as we expect them to."

Black stares at Sellers, trying to find some source of empathy in the man's intense gaze. He finds nothing, but he finds himself mirroring that intensity. Of course he wants to know what they could pull from the ashes of this forgotten project. Maybe if he needed to, he could get out of the situation before it became too much. "What's the plan?"

* * *

Shadow POV_

I never like being on missions with Knuckles. Honestly, he doesn't think before he does anything and it's a miracle he isn't constantly walking into walls and off cliffs. He doesn't pay atten-

"Why exactly are we here, again?" he asks, with perfect timing as always.

We're a couple miles outside the city, where Tails apparently detected some chaos signals. I'm nearly always sent on these kinds of missions, and usually I'm with someone who's a little more... not Knuckles. "Chaos signals," I tell him vaguely. Something feels like it's creeping up on me and I stop walking and turn around, scanning the grounds. Knuckles does the same, and says my name quietly.

"Did you hear something?" he asks.

I keep staring back, watching everything someone could hide behind for a few seconds. "No, I just wanted to take in the beautiful scenery, of course." Sometimes he can't tell when I'm using sarcasm, so he just doesn't respond. To clarify, I say, "yes, I thought I heard something."

We continue walking, and the chaos sensor on my wrist still indicates a small source of energy somewhere nearby.

"I'm not seeing anything," Knuckles shrugs. I almost respond, but I hear that same sound again, closer. A light snapping sound, somewhere behind us, to the right.

"Sh," I look exactly in the direction the sound came from, and a flicker of motion a few feet to the left catches my attention. Something's coming straight at me, and I drop quick enough to avoid being hit. Of course, it hits Knuckles instead. The echidna cusses at the sudden sting of pain, and I glance at him. He's pulling something out of his chest. It's a tranquilizer dart..?

I stand back up and the chaos in my body rushes to my palm. I force the chaos outwards, and a shower of chaos spears cover the ground where the dart came from. Somebody yells and suddenly there's movement everywhere. Men in uniforms? My favorite..

Knuckles is bound to pass out any second - that's great. Three more darts come toward me in quick succession, and I'm able to avoid all of them by jumping back. A fourth flies by my stomach from the side, and I nearly fall backwards to avoid it. They're obviously trying to hit _me_, and it seems like Knuckles isn't even part of their concern. Fiery chaos collects in my chest, and a crimson wave of energy pulses out from me, scorching the ground and two of the men were engulfed in flames. They start yelling and drop their guns, and six other men are still coming at us.

I use chaos control and appear beside Knuckles. He's already finding it difficult to stand.

"Th-they're on fire," Knuckles says, disoriented. Quickly in my mind, I realize their goal isn't to kill either of us. There's a reason these are just tranquilizers. They want me alive. I push Knuckles (somewhat lightly) onto the ground so he won't injure himself when he loses consciousness, and as I turn back towards the GUN soldiers, I release another several chaos spears, and I see those two soldiers covered in flames - well, I hear them. Screaming. It's not a pleasant sound, but it doesn't bother me much. Not when those uniforms are burning along with them..

I hear the clicking of a loaded gun, and my attention turns to a soldier. His gun isn't pointed at me, but straight at Knuckles, who's a few yards behind me.

"You're coming with us, Shadow! Refusal will result in the death of your friend," the gunman tells me. Hatred burns in my veins at the poisonous familiarity of this situation. As much as Knuckles annoys me, I can't let the past repeat itself. "You have five seconds!"

Five seconds to come up with an idea that won't kill either of us. Why do they want me this time? How did they even know where we are?

"Four!"

I see the burning men on the ground. They stopped screaming a moment ago. Luckily, they're downwind.

"Three!"

No one has tranquilized me, and I've been standing here..

"Two!"

"If you shoot him, I'll make sure you're all dead within the hour."

"One-"

I step between Knuckles and the gunned soldier and put my arms out in a reluctant indication of compliance. I so badly want to just kill all of them. I make sure to see and memorize the eyes of the gunman. Light green. Easy enough to remember. He'll die first. He lowers his gun just an inch. "Come closer!" he tells me.

I glare at him, not about to take orders, and I activate the communicator on my wrist. It flashes white once, indicating Tails can hear me. "Listen, Tails."

"Shadow? You sound..."

"Take note of where I am," I tell him. The gunman yells something like I need to obey, and I give him a look that clearly tells him to fuck off. "Knuckles will be here. GUN tranquilized him, but he should be fine otherwise."

"Shadow, wait, what's going on!?" Tails asks, fully attentive.

I look up, making sure all of these stupid men are listening. "If Knuckles isn't here, or if he's at all injured, let me know. I'll make sure whatever happens is repaid."

"Shadow?" a different voice calls me. It's Sonic, and suddenly I feel... different. I don't want to talk to either of them. "Tell me right now what's wrong? It's GUN?"

I glance up again, and the gunman hasn't moved an inch. He looks pretty pissed though, which would've made me smile if we weren't in this situation.

"We're not waiting any longer!" he tells me.

"Sonic, I have to go. Make sure Knuckles is safe." I turn off the communicator, not wanting to hear Sonic's objections and confusion.


	3. Burning

Sonic POV_

When the white light on Tails' communicator faded, I put my hands up by my ears, suddenly overwhelmed. "What is he talking about? Where is he?"

"I'm tracking his location right now," Tails responds, pressing buttons on the communicator while I tried to think about every word Shadow said.

"GUN? What'd he say about them? He didn't.. why didn't he let us know what was going on?" I look at the communicator, and the red dots on the screen aren't clear enough for me to recognize exactly where they are. "Where are they? I need to go, now."

"Sonic, give it at least a few minutes. Shadow can defend himself. He said Knuckles would be there, though, so make sure the coast is clear before you-"

"Tails, I'm not going to wait. I need to go. Where is it?" I cross my arms, too wound up to know what else to do. Tails gives me a concerned look with his big blue eyes, and it just increases my unease.

Tails looks down at the device, and decides, "they're just outside the city, near the woods. Just west of the lake." He looks up at me and adds, "please be careful. If you only find Knuckles there, bring him back here before you go off and do anything crazy."

"Yeah, alri-"

Three high pitched beeps emit from the communicator, and the red dot vanishes. "Oh," Tails mumbles.

"'Oh' what?"

Tails taps the screen and says, "I just lost connection with Shadow. Either he turned it off completely, or it was damaged."

Heat and nerves light up my senses, and I leave MPA and head in the direction of the last transmission as fast as I can.

* * *

Shadow POV_

The gunman keeps the barrel pointed at me as I disconnect with Tails. I know he's not going to fire. He would've before now if he intended to, and it's clear they want me for some reason. Alive.

"Let's move!" one of them say. I see that one glance at one of the still-burning bodies, a little shocked. Maybe it was a friend.

"Come on," the green eyed man tells me, motioning the direction with his gun. Every ounce of me is dying to just turn that gun in his hand around and make him shoot himself.. but as soon as I react even slightly like that, they'll probably shoot Knuckles and I'd have his blood on my hands. That wouldn't help anything. My body reacts and I start walking away, following some of the other soldiers who were already beginning to leave. I keep an eye on the gunned man behind me, making sure he doesn't point it toward Knuckles. He's definitely fixed on me, so I'm not as concerned. I'm sure Sonic's already on his way out here. Knuckles should be fine.

Before long, we are far enough to not see the fire on the two soldiers' bodies. While glancing back to notice that, the green eyed man stops and tells me to leave the communicator here at this point. Sonic and Tails should know vaguely where they're taking me. Besides, Tails' chaos detectors should pick up on me easily. I pull the screened bracelet off my wrist, break the screen in my fist, and drop it on the ground. I hold his gaze while I do this, making sure he knows how useless what he's doing is. It doesn't bother me at all. He stares back, narrowing his eyes, easily sensing my indifference. It's annoying him. I laugh and turn around and continue walking. A single gunshot fires, and it's clear that he shot the communicator just to make sure it would be destroyed. The soldiers in front of us turned around, wondering what happened. They realize I wasn't shot, and their attention turns back to the trek.

As careless as I'm making myself seem, the closer we get to GUN's HQ, the more intense my memories of the ARK become. Needles. Drugs. Blood. I touch my inner forearm and take a deep breath, trying to prep myself mentally for whatever they're going to try with me.

* * *

Sonic POV_

Fire in the distance catches my attention. It's a low burn, and something in the air smells like death and something else that's horrible. There's the smallest speck of red just beyond the flames - Knuckles.

In a flash, I'm near the clearing. Knuckles is out, laying on the ground like it's a simple summer day. From the two melting bodies a couple meters away, it was clear that today wasn't the simplest. I try not to inhale and I walk to Knuckles' side. I shake his shoulder, but the tranquilizer Shadow mentioned is still in full effect.

"Knuckles! Come on, wake up..." I attempt. His eyes don't open even slightly, but he mumbles something about burning. Good, he's alright. I shake him again, calling his name. "It's gonna be pretty difficult for me to carry you all the way back to Tails!"

The echidna doesn't even stir. I cover my face and sigh as deeply as I could without inhaling that horrific scent, and I turn on my communicator. "Tails."

"Sonic! Did you find them?" Tails asks with urgency in his voice.

"I found Knuckles, not Shadow." I hear crackling in the fire, and this is almost too much for me to deal with. "Tails, there are two burning bodies here, two men," I tell him. "No blood anywhere, but I need to get out of here. I'll be back as soon as possible."

I disconnect the conversation, and I lean over Knuckles again and smack him across the face. "Knuckles!"

"...he pushed me down," Knuckes mutters. "...damn darts."

"Knuckles, come on..." I stand up, pulling on his arm, and he finally opens his eyes a bit. "Hey! Hey, stay awake, stay with me." I lean down and tell him, "you gotta get up. We need to get back to MPA right now."

"MPA..?" he mumbles.

"Yeah, we live there," I tell him, losing patience. I force him up to his feet and his weight nearly knocks me down. "Walk. Let's go."

Anyone who complains of experiencing difficult tasks has never walked a tranquilized echidna twice his weight over fifty miles. Fortunately, he became more and more coherent as we went, and by the time we were approaching the city, he could walk without any support from me.

"What happened?" I ask him, hoping he was awake for everything.

"GUN ambushed us," Knuckles tells me. "I think they just wanted me out of the way."

My thoughts are consumed by Shadow. "Is he okay?" I ask.

"Shadow? I don't know. He.."

"He what?"

"I don't remember well. I know he was fighting back. There was fire," Knuckles says. "People on fire."

"Yeah, I know that," I respond, short on patience and disturbed by the image. "What else?"

Knuckles shrugs. "Shadow pushed me down a few seconds after they hit me with the stupid tranquilizer."

"Why?" I ask. Knuckles just shrugs again. Frustration wells up in me. Shadow could be in serious danger. "As soon as we get you back to Tails, I'm going to go find him."

We're finally in the infirmary, and Tails is going over Knuckles, making sure he's in good health. Meanwhile, I'm unable to focus. I need to figure out what's going on and what happened.

"For the eightieth time, Sonic. There's no way of knowing where they went," Tails tells me.

I roll my eyes and cross my arms, suddenly feeling a lot like Shadow. "So what are we gonna do?"

Tails turns to Knuckles and says, "everything seems alright. Thanks." He turns to me and sighs. "I don't know, Sonic. Sounds like GUN gave Shadow an ultimatum, and Shadow chose to keep Knuckles alive and go with them. I'm pretty sure GUN has a lot of places to hide, but I don't see why they wouldn't go back to their normal HQ."

"So, we should check with their HQ," I say.

"That's a little suspicious," Tails responds with a hint of sarcasm.

Suddenly Rouge enters the room, looking upset. "Hey! I was looking for you!" she says, looking primarily at me. "All of you! What's going on with Shadow? GUN just announced he has been incarcerated for murder?"

I turn to Knuckles immediately, and his eyes are wide. "Did Shadow burn those people intentionally?" I ask.

"Burn!?" I hear Rouge say. Knuckles just slightly shrugs and shakes his head.

"You know it's possible," the echidna says. "We all know how much he hates GUN."

"He wouldn't kill someone unless he had a reason to," I tell them. I feel like all of them just melted right into Knuckles' words - 'we all know how much he hates GUN.' "You know, from the way it looks, he saved your life less than an hour ago, and you're already saying he's guilty of something you weren't even coherent enough to see!"

"Oh, chaos..." Rouge murmurs from the doorway, apparently absorbing all of this information and becoming overwhelmed by the sudden intensity of everything.

"You're honestly telling me you couldn't see him possibly killing someone without a real reason?" Knuckles asks me, still on the table Tails had him lay down on. If he stood up, he'd probably be in my face. "Like you haven't seen him do it before?"

"Knuckles, what the hell is wrong with you?" I'm pissed at this point! Who does he think he is? "Do you have any idea who he really is?" Knuckles opens his mouth to reply, but I speak over him and he just stops and lets me go. "Shadow has one hell of an exterior, you know. He hates getting close to people, he hates letting them in. But you know, if you'd just give him a chance, maybe he'd open up to you like he has to me! You have no idea how much death and murder bother him! Absolutely no idea!"

Tails tries to get between Knuckles and I. "Sonic, uh.."

"He hates it so much, he does it anyway!" Knuckles yells back.

I really, really have to fight the urge to punch Knuckles right in the mouth. I leave the room, walking past Rouge without looking at her. I take one of the deepest, shakiest breaths I've taken in a while, and anger still pulses through me. The worst part about this, is I know there's truth to what Knuckles is saying.

Shadow was never meant to be a murderer, but his time on the ARK really made that hard to believe.

* * *

**Hey readers! :) I'm pretty new to this, but hopefully this is interesting to some of you so far. Reviews mean the whole world to me, so feel free to leave one! Thanks for reading! ~dripping-glass**


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